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Structure of agra lyttr domain in complex with promoters

Analyse Structure of agra lyttr domain in complex with promoters in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4XXE
Type: protein + DNA
Length: 254 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Accessory gene regulator a; DNA (5'-D(P*TP*AP*CP*AP*GP*TP*TP*AP*GP*GP*CP*AP*A)-3'); DNA…
UniProt: Q5HEG2
Pockets: 5 · best druggability 0.79

Structure

x-ray diffraction · 4 distinct chains · 15% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D	Accessory gene regulator a	protein	99	15% helix, 48% strand	Q5HEG2
B	DNA (5'-D(PTPAPCPAPGPTPTPAPGPGPCPAP*A)-3')	dna	13	—	—
C, F	DNA (5'-D(APTPTPGPCPCPTPAPAPCPTPGPTPAP*G)- 3')	dna	15	—	—
E	DNA (5'-D(PTPAPCPAPGPTPTPAPGPGPCPAP*T)-3')	dna	13	—	—

Pockets

5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	910	0.79	0.81	82	empty
2	120	0.38	0.75	15	empty
3	96	0.37	0.76	15	empty
4	73	0.33	0.75	14	empty
5	54	0.27	0.74	10	empty

Interfaces

11 interfaces between chains.

A–D · 625 Å² buried · 7 hydrogen bonds · protein-protein
B–C · 611 Å² buried · 45 hydrogen bonds · nucleic-nucleic
E–F · 603 Å² buried · 45 hydrogen bonds · nucleic-nucleic
A–C · 511 Å² buried · 8 hydrogen bonds · protein-nucleic
D–F · 442 Å² buried · 9 hydrogen bonds · protein-nucleic

Compared structures

4XXE · Structure of AgrA LytTR domain in complex with promoters · the same entry in another collection · chain F against F, TM-score 1.00
Q5HEG2 · AlphaFold monomer V2.0 prediction for accessory gene regulator a (Q5HEG2) · a predicted model of the same protein · chain D against A, TM-score 0.97

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q5HEG2
Elsewhere: RCSB PDB 4XXE · PDBe 4XXE · UniProt Q5HEG2

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